broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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Running infercnv on a large dataset #572

Open ConDem94 opened 1 year ago

ConDem94 commented 1 year ago

Hello, I'm trying to run infercnv for a large integrated dataset with 93+ samples (270,000 cells), however I am running out of memory and the run crashes even by running it in a cluster with parallel computing. I have set the parameters to default based on the available vignettes and video tutorial.

Is there a way to run this code with this much cells faster and use less memory? Will skipping some analyses, such as setting HMM=FALSE, make it run faster?

I can provide my code as well, but was wondering if there is an easy solution to this.

Best wishes, Constantinos

julie-jch commented 1 year ago

@ConDem94 Did you ever figure out a solution to this problem?